RetrogeneDB ID: retro_ggor_453

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:158187130..158188110(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ENSG00000175354
• Ensembl ID: ENSGGOG00000010259
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:G3R421]

Sequence

>retro_ggor_453
GATCACAGTTGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGACAAAGG
AGTTACATCTTAACACAGGGTCCACTTCCTAACACATGCTGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGC
AGCTGTCATGCTGAACCGCATTACGGAGAAAGAATTAGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAGAGATGC
TGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACCACAATTA
GAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACTTGGCCAGATTTTGGAGTCCCTCAATC
ACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGACCTGCGGTGATCC
ACCGTAGTGCAGGCACTGGACGCTCCAGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGATGAT
ATTAACATTAAACAAGTGTTACTGAACGTAAGAAAATTCCGAATGGGTCTTATCTCGGACCGCAGATCAACTGAGATTCT
CATACATGGCTATAATAGAAGGAGCAAAATGTGTAAAGGGAGATTCTAGTATACAGAAACGATGGAAAGAACTTTCTAAG
GAAGACTACCTCCTGCTTTTGATCACTCACCAAACAAAATAATGACTGAAAAATACAATAGGAACAGAATAGGTCTAGAA
GAAGAAAAACTGACAGGTGACTGACGTACAGGACTTTCCTCTAAAATGCAAGATACAATGGAGGAGAACAATGAGAGTGT
TCTACGGAAACGTATGTGAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAATAGAGGCTAAATGAGA
ATGAACGAAAAAGAAAAAGG

Alignment

ORF - retro_ggor_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 78.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DHSRVKLQNAENDYINASLVDIEE-AQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKC
          DHS.VKLQNAENDYINASLVDIEE..QRSYILTQGPLPNTCCHFWLMVWQQKTKA.VMLNRI.EKE.VKC
Retrocopy DHSCVKLQNAENDYINASLVDIEE<GQRSYILTQGPLPNTCCHFWLMVWQQKTKAAVMLNRITEKELVKC

Parental  AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFL
          AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHL.QLENINSGETRTISHFHYTTWPDFGVP.SPASFL
Retrocopy AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLPQLENINSGETRTISHFHYTTWPDFGVPQSPASFL

Parental  NFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLI-QTP
          NFLFKVRESGSLNPDHGPAVIH.SAG.GRS.TFSLVDTCLVLMEKGDDINIKQVLLN.RK.RMGLI..T.
Retrocopy NFLFKVRESGSLNPDHGPAVIHRSAGTGRSSTFSLVDTCLVLMEKGDDINIKQVLLNVRKFRMGLI>RTA

Parental  DQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED-LSPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCT
          DQLRFSYMAIIEGAKC.KGDSSIQKRWKELSKED.L.PAFDHSPNKIMTEKYN.NRIGLEEEKLTGD..T
Retrocopy DQLRFSYMAIIEGAKCVKGDSSIQKRWKELSKED<LPPAFDHSPNKIMTEKYNRNRIGLEEEKLTGD*RT

Parental  GLSSKMQDTMEENSESALRKRIREDRKATTAQKVQQMKQRLNENERKRKR
          GLSSKMQDTMEEN.ES.LRKR..EDRKATTAQKVQQMK.RLNENERKRKR
Retrocopy GLSSKMQDTMEENNESVLRKRM*EDRKATTAQKVQQMK*RLNENERKRKR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.55 RPM
SRP007412_cerebellum	0.04 RPM	5.44 RPM
SRP007412_heart	0.00 RPM	0.66 RPM
SRP007412_kidney	0.00 RPM	6.87 RPM
SRP007412_liver	0.00 RPM	4.01 RPM
SRP007412_testis	0.00 RPM	9.22 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453 , retro_ggor_925,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,